Starting phenix.real_space_refine on Sat Nov 16 08:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvt_35048/11_2024/8hvt_35048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvt_35048/11_2024/8hvt_35048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvt_35048/11_2024/8hvt_35048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvt_35048/11_2024/8hvt_35048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvt_35048/11_2024/8hvt_35048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvt_35048/11_2024/8hvt_35048.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6952 2.51 5 N 1730 2.21 5 O 1940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10702 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3653 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 17, 'TRANS': 462} Chain breaks: 1 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1617 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 2 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3653 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 17, 'TRANS': 462} Chain breaks: 1 Chain: "D" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1617 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.38, per 1000 atoms: 0.60 Number of scatterers: 10702 At special positions: 0 Unit cell: (90.47, 115.37, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 1940 8.00 N 1730 7.00 C 6952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.04 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 115 " distance=2.04 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 174 " - pdb=" SG CYS D 255 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG B 401 " - " ASN B 128 " " NAG B 402 " - " ASN B 163 " " NAG B 403 " - " ASN B 194 " " NAG D 401 " - " ASN D 128 " " NAG D 402 " - " ASN D 163 " " NAG D 403 " - " ASN D 194 " " NAG E 1 " - " ASN D 263 " " NAG F 1 " - " ASN B 263 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 75.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 119 through 164 Processing helix chain 'A' and resid 172 through 197 removed outlier: 3.693A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.622A pdb=" N ALA A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.842A pdb=" N LEU A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.675A pdb=" N SER A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.596A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 removed outlier: 4.046A pdb=" N GLU A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.569A pdb=" N MET A 368 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 374 through 406 Processing helix chain 'A' and resid 409 through 434 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.652A pdb=" N PHE A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.591A pdb=" N VAL A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 506 removed outlier: 4.663A pdb=" N GLY A 506 " --> pdb=" O CYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 536 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.570A pdb=" N TYR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'A' and resid 580 through 596 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'B' and resid 81 through 105 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 115 through 130 Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.058A pdb=" N MET B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.572A pdb=" N LEU B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 201 removed outlier: 3.719A pdb=" N VAL B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 245 removed outlier: 3.683A pdb=" N GLU B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 281 through 305 removed outlier: 3.803A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'C' and resid 119 through 164 Processing helix chain 'C' and resid 172 through 197 removed outlier: 3.693A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.622A pdb=" N ALA C 202 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.842A pdb=" N LEU C 227 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 262 removed outlier: 3.675A pdb=" N SER C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 302 removed outlier: 3.596A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 314 removed outlier: 4.046A pdb=" N GLU C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 346 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.569A pdb=" N MET C 368 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 369 " --> pdb=" O GLU C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 369' Processing helix chain 'C' and resid 374 through 406 Processing helix chain 'C' and resid 409 through 434 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.652A pdb=" N PHE C 466 " --> pdb=" O MET C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 removed outlier: 3.591A pdb=" N VAL C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 506 removed outlier: 4.663A pdb=" N GLY C 506 " --> pdb=" O CYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 536 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.570A pdb=" N TYR C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 Processing helix chain 'C' and resid 580 through 596 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'D' and resid 81 through 105 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 144 through 148 removed outlier: 4.058A pdb=" N MET D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 148' Processing helix chain 'D' and resid 153 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.572A pdb=" N LEU D 175 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 201 removed outlier: 3.719A pdb=" N VAL D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 245 removed outlier: 3.683A pdb=" N GLU D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 270 Processing helix chain 'D' and resid 281 through 305 removed outlier: 3.803A pdb=" N VAL D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 439 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 439 746 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2870 1.33 - 1.46: 2832 1.46 - 1.58: 5118 1.58 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 10942 Sorted by residual: bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 NAG D 402 " pdb=" O5 NAG D 402 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CG LEU A 587 " pdb=" CD1 LEU A 587 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.98e+00 bond pdb=" CG LEU C 587 " pdb=" CD1 LEU C 587 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.98e+00 bond pdb=" CB ASN C 339 " pdb=" CG ASN C 339 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.07e+00 ... (remaining 10937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 13988 2.08 - 4.16: 708 4.16 - 6.25: 114 6.25 - 8.33: 40 8.33 - 10.41: 16 Bond angle restraints: 14866 Sorted by residual: angle pdb=" CA ARG D 104 " pdb=" CB ARG D 104 " pdb=" CG ARG D 104 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CA ARG B 104 " pdb=" CB ARG B 104 " pdb=" CG ARG B 104 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" C ARG D 107 " pdb=" N PRO D 108 " pdb=" CA PRO D 108 " ideal model delta sigma weight residual 119.84 114.96 4.88 1.25e+00 6.40e-01 1.52e+01 angle pdb=" C ARG B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.84 114.96 4.88 1.25e+00 6.40e-01 1.52e+01 angle pdb=" C SER D 276 " pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta sigma weight residual 122.13 129.04 -6.91 1.85e+00 2.92e-01 1.40e+01 ... (remaining 14861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 6112 23.20 - 46.41: 382 46.41 - 69.61: 38 69.61 - 92.81: 28 92.81 - 116.01: 10 Dihedral angle restraints: 6570 sinusoidal: 2644 harmonic: 3926 Sorted by residual: dihedral pdb=" CA PRO D 108 " pdb=" C PRO D 108 " pdb=" N VAL D 109 " pdb=" CA VAL D 109 " ideal model delta harmonic sigma weight residual 180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PRO B 108 " pdb=" C PRO B 108 " pdb=" N VAL B 109 " pdb=" CA VAL B 109 " ideal model delta harmonic sigma weight residual 180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASN D 177 " pdb=" C ASN D 177 " pdb=" N ASN D 178 " pdb=" CA ASN D 178 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 6567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1320 0.063 - 0.125: 352 0.125 - 0.188: 76 0.188 - 0.250: 20 0.250 - 0.313: 4 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CB VAL C 513 " pdb=" CA VAL C 513 " pdb=" CG1 VAL C 513 " pdb=" CG2 VAL C 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL A 513 " pdb=" CA VAL A 513 " pdb=" CG1 VAL A 513 " pdb=" CG2 VAL A 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1769 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 515 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO C 516 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 515 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 516 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 81 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO B 82 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.032 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2960 2.80 - 3.33: 10308 3.33 - 3.85: 17728 3.85 - 4.38: 19636 4.38 - 4.90: 34707 Nonbonded interactions: 85339 Sorted by model distance: nonbonded pdb=" OG SER A 290 " pdb=" OG SER A 311 " model vdw 2.279 3.040 nonbonded pdb=" OG SER C 290 " pdb=" OG SER C 311 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR B 176 " pdb=" O ASN B 178 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR D 176 " pdb=" O ASN D 178 " model vdw 2.284 3.040 nonbonded pdb=" OG SER C 476 " pdb=" OD2 ASP C 480 " model vdw 2.289 3.040 ... (remaining 85334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.540 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 10942 Z= 0.566 Angle : 1.108 10.411 14866 Z= 0.579 Chirality : 0.064 0.313 1772 Planarity : 0.007 0.081 1838 Dihedral : 16.297 116.015 4018 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.18), residues: 1346 helix: -1.04 (0.14), residues: 932 sheet: None (None), residues: 0 loop : -2.88 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 524 HIS 0.011 0.003 HIS C 479 PHE 0.028 0.002 PHE A 363 TYR 0.018 0.002 TYR A 448 ARG 0.009 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.6427 (mttp) cc_final: 0.5278 (pttp) REVERT: A 471 GLU cc_start: 0.8171 (mp0) cc_final: 0.7800 (mp0) REVERT: C 367 LYS cc_start: 0.6465 (mttp) cc_final: 0.5303 (pttp) REVERT: C 471 GLU cc_start: 0.8173 (mp0) cc_final: 0.7792 (mp0) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2142 time to fit residues: 67.1257 Evaluate side-chains 168 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.179 Angle : 0.661 8.342 14866 Z= 0.341 Chirality : 0.042 0.154 1772 Planarity : 0.005 0.067 1838 Dihedral : 11.281 102.404 1698 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.87 % Allowed : 9.95 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1346 helix: 0.96 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.66 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 524 HIS 0.004 0.001 HIS A 479 PHE 0.014 0.001 PHE C 392 TYR 0.013 0.001 TYR A 505 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 210 average time/residue: 0.1511 time to fit residues: 47.1936 Evaluate side-chains 186 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 359 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10942 Z= 0.221 Angle : 0.632 8.455 14866 Z= 0.322 Chirality : 0.043 0.165 1772 Planarity : 0.005 0.062 1838 Dihedral : 9.865 100.145 1698 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.57 % Allowed : 12.57 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1346 helix: 1.64 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.60 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 524 HIS 0.003 0.001 HIS A 605 PHE 0.015 0.001 PHE C 392 TYR 0.013 0.001 TYR A 505 ARG 0.008 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 HIS cc_start: 0.8361 (t70) cc_final: 0.8095 (t70) REVERT: D 195 HIS cc_start: 0.8361 (t70) cc_final: 0.8092 (t70) outliers start: 18 outliers final: 12 residues processed: 206 average time/residue: 0.2128 time to fit residues: 63.9399 Evaluate side-chains 196 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10942 Z= 0.155 Angle : 0.608 8.678 14866 Z= 0.306 Chirality : 0.041 0.193 1772 Planarity : 0.004 0.058 1838 Dihedral : 8.844 98.010 1698 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.40 % Allowed : 14.49 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1346 helix: 2.02 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.50 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 524 HIS 0.004 0.001 HIS A 605 PHE 0.012 0.001 PHE A 392 TYR 0.013 0.001 TYR C 505 ARG 0.007 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 HIS cc_start: 0.8252 (t70) cc_final: 0.8028 (t70) REVERT: D 195 HIS cc_start: 0.8254 (t70) cc_final: 0.8029 (t70) outliers start: 16 outliers final: 8 residues processed: 204 average time/residue: 0.2176 time to fit residues: 64.7401 Evaluate side-chains 194 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 186 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10942 Z= 0.215 Angle : 0.603 8.697 14866 Z= 0.306 Chirality : 0.042 0.169 1772 Planarity : 0.005 0.058 1838 Dihedral : 8.400 96.940 1698 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.18 % Allowed : 15.10 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1346 helix: 2.18 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 524 HIS 0.004 0.001 HIS B 195 PHE 0.024 0.001 PHE D 200 TYR 0.011 0.001 TYR A 505 ARG 0.010 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.258 Fit side-chains REVERT: A 368 MET cc_start: 0.6665 (ptm) cc_final: 0.6396 (ptp) REVERT: B 168 GLU cc_start: 0.8390 (tp30) cc_final: 0.7890 (mm-30) REVERT: B 174 CYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5873 (m) REVERT: B 238 MET cc_start: 0.9048 (mtm) cc_final: 0.8766 (mtp) REVERT: C 368 MET cc_start: 0.6665 (ptm) cc_final: 0.6393 (ptp) REVERT: D 168 GLU cc_start: 0.8383 (tp30) cc_final: 0.7886 (mm-30) REVERT: D 174 CYS cc_start: 0.6180 (OUTLIER) cc_final: 0.5871 (m) REVERT: D 238 MET cc_start: 0.9045 (mtm) cc_final: 0.8762 (mtp) outliers start: 25 outliers final: 14 residues processed: 197 average time/residue: 0.2314 time to fit residues: 66.7655 Evaluate side-chains 194 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.188 Angle : 0.609 9.079 14866 Z= 0.304 Chirality : 0.041 0.155 1772 Planarity : 0.004 0.057 1838 Dihedral : 8.083 95.211 1698 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.18 % Allowed : 15.45 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1346 helix: 2.34 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.43 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 PHE 0.019 0.001 PHE B 200 TYR 0.011 0.001 TYR A 505 ARG 0.012 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.173 Fit side-chains REVERT: A 198 GLU cc_start: 0.8012 (tp30) cc_final: 0.7743 (tp30) REVERT: A 368 MET cc_start: 0.6677 (ptm) cc_final: 0.6377 (ptp) REVERT: A 451 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: B 168 GLU cc_start: 0.8381 (tp30) cc_final: 0.7920 (mm-30) REVERT: B 174 CYS cc_start: 0.5971 (OUTLIER) cc_final: 0.5624 (m) REVERT: B 197 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8755 (mm) REVERT: C 198 GLU cc_start: 0.8017 (tp30) cc_final: 0.7751 (tp30) REVERT: C 368 MET cc_start: 0.6673 (ptm) cc_final: 0.6372 (ptp) REVERT: C 451 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: D 168 GLU cc_start: 0.8374 (tp30) cc_final: 0.7916 (mm-30) REVERT: D 174 CYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5621 (m) REVERT: D 197 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8757 (mm) outliers start: 25 outliers final: 16 residues processed: 197 average time/residue: 0.2145 time to fit residues: 61.1553 Evaluate side-chains 198 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.0010 chunk 52 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10942 Z= 0.164 Angle : 0.591 8.991 14866 Z= 0.296 Chirality : 0.041 0.157 1772 Planarity : 0.004 0.056 1838 Dihedral : 7.855 93.460 1698 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.92 % Allowed : 16.58 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1346 helix: 2.59 (0.16), residues: 942 sheet: None (None), residues: 0 loop : -2.31 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 PHE 0.012 0.001 PHE C 392 TYR 0.010 0.001 TYR C 505 ARG 0.013 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.128 Fit side-chains REVERT: A 332 MET cc_start: 0.8605 (tpt) cc_final: 0.8255 (tpt) REVERT: A 368 MET cc_start: 0.6649 (ptm) cc_final: 0.6334 (ptp) REVERT: A 451 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: B 168 GLU cc_start: 0.8387 (tp30) cc_final: 0.7910 (mm-30) REVERT: B 262 MET cc_start: 0.8444 (mmm) cc_final: 0.8003 (tmm) REVERT: B 281 ASP cc_start: 0.7686 (p0) cc_final: 0.7239 (t70) REVERT: C 332 MET cc_start: 0.8606 (tpt) cc_final: 0.8257 (tpt) REVERT: C 368 MET cc_start: 0.6567 (ptm) cc_final: 0.6243 (ptp) REVERT: C 451 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: D 168 GLU cc_start: 0.8378 (tp30) cc_final: 0.7904 (mm-30) REVERT: D 262 MET cc_start: 0.8444 (mmm) cc_final: 0.8003 (tmm) REVERT: D 281 ASP cc_start: 0.7686 (p0) cc_final: 0.7243 (t70) outliers start: 22 outliers final: 15 residues processed: 199 average time/residue: 0.2140 time to fit residues: 62.0968 Evaluate side-chains 203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10942 Z= 0.163 Angle : 0.605 9.077 14866 Z= 0.300 Chirality : 0.041 0.159 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.735 92.018 1698 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.48 % Allowed : 18.06 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1346 helix: 2.67 (0.16), residues: 942 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 524 HIS 0.005 0.001 HIS B 195 PHE 0.012 0.001 PHE C 392 TYR 0.009 0.001 TYR C 448 ARG 0.008 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 1.238 Fit side-chains REVERT: A 332 MET cc_start: 0.8607 (tpt) cc_final: 0.8249 (tpt) REVERT: A 368 MET cc_start: 0.6636 (ptm) cc_final: 0.6301 (ptp) REVERT: A 451 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 168 GLU cc_start: 0.8378 (tp30) cc_final: 0.7817 (mm-30) REVERT: C 332 MET cc_start: 0.8604 (tpt) cc_final: 0.8252 (tpt) REVERT: C 368 MET cc_start: 0.6636 (ptm) cc_final: 0.6300 (ptp) REVERT: C 451 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: D 168 GLU cc_start: 0.8374 (tp30) cc_final: 0.7812 (mm-30) outliers start: 17 outliers final: 13 residues processed: 196 average time/residue: 0.2069 time to fit residues: 60.0763 Evaluate side-chains 191 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10942 Z= 0.167 Angle : 0.608 9.177 14866 Z= 0.303 Chirality : 0.041 0.156 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.641 90.406 1698 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.31 % Allowed : 18.59 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.23), residues: 1346 helix: 2.64 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 524 HIS 0.005 0.001 HIS B 195 PHE 0.020 0.001 PHE B 193 TYR 0.015 0.001 TYR C 448 ARG 0.007 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 1.186 Fit side-chains REVERT: A 332 MET cc_start: 0.8602 (tpt) cc_final: 0.8243 (tpt) REVERT: A 368 MET cc_start: 0.6621 (ptm) cc_final: 0.6279 (ptp) REVERT: A 451 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 168 GLU cc_start: 0.8350 (tp30) cc_final: 0.7954 (mm-30) REVERT: B 262 MET cc_start: 0.8419 (mmm) cc_final: 0.8011 (tmm) REVERT: B 281 ASP cc_start: 0.7594 (p0) cc_final: 0.7179 (t70) REVERT: C 332 MET cc_start: 0.8601 (tpt) cc_final: 0.8248 (tpt) REVERT: C 368 MET cc_start: 0.6616 (ptm) cc_final: 0.6274 (ptp) REVERT: C 451 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8302 (pt0) REVERT: D 168 GLU cc_start: 0.8343 (tp30) cc_final: 0.7948 (mm-30) REVERT: D 262 MET cc_start: 0.8418 (mmm) cc_final: 0.8012 (tmm) REVERT: D 281 ASP cc_start: 0.7585 (p0) cc_final: 0.7185 (t70) outliers start: 15 outliers final: 11 residues processed: 196 average time/residue: 0.2153 time to fit residues: 61.1261 Evaluate side-chains 195 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10942 Z= 0.245 Angle : 0.663 11.289 14866 Z= 0.326 Chirality : 0.043 0.156 1772 Planarity : 0.004 0.056 1838 Dihedral : 7.666 89.811 1698 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.22 % Allowed : 19.02 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.23), residues: 1346 helix: 2.57 (0.16), residues: 944 sheet: None (None), residues: 0 loop : -2.15 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 524 HIS 0.004 0.001 HIS B 195 PHE 0.020 0.001 PHE B 193 TYR 0.013 0.001 TYR C 448 ARG 0.008 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 1.167 Fit side-chains REVERT: A 368 MET cc_start: 0.6648 (ptm) cc_final: 0.6305 (ptp) REVERT: A 451 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: B 104 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8218 (mmt90) REVERT: B 168 GLU cc_start: 0.8339 (tp30) cc_final: 0.7939 (mm-30) REVERT: B 262 MET cc_start: 0.8458 (mmm) cc_final: 0.8034 (tmm) REVERT: C 368 MET cc_start: 0.6652 (ptm) cc_final: 0.6307 (ptp) REVERT: C 451 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: D 104 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8218 (mmt90) REVERT: D 168 GLU cc_start: 0.8334 (tp30) cc_final: 0.7938 (mm-30) REVERT: D 262 MET cc_start: 0.8458 (mmm) cc_final: 0.8032 (tmm) outliers start: 14 outliers final: 10 residues processed: 192 average time/residue: 0.2249 time to fit residues: 62.7563 Evaluate side-chains 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.0170 chunk 15 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.108594 restraints weight = 14278.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.112019 restraints weight = 8434.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.114191 restraints weight = 6054.361| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10942 Z= 0.147 Angle : 0.611 9.475 14866 Z= 0.301 Chirality : 0.040 0.148 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.423 86.469 1698 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.87 % Allowed : 19.20 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.23), residues: 1346 helix: 2.61 (0.16), residues: 952 sheet: None (None), residues: 0 loop : -2.01 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 524 HIS 0.004 0.001 HIS D 195 PHE 0.014 0.001 PHE D 193 TYR 0.014 0.001 TYR C 448 ARG 0.008 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.91 seconds wall clock time: 60 minutes 22.35 seconds (3622.35 seconds total)